Starting phenix.real_space_refine on Tue Aug 6 00:47:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/08_2024/8vwp_43593.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/08_2024/8vwp_43593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/08_2024/8vwp_43593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/08_2024/8vwp_43593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/08_2024/8vwp_43593.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/08_2024/8vwp_43593.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 9592 2.51 5 N 2500 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 398": "NH1" <-> "NH2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "D ARG 463": "NH1" <-> "NH2" Residue "D TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 466": "NH1" <-> "NH2" Residue "D TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 599": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14820 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3691 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 476} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3691 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 476} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 129 Chain: "C" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3691 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 476} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 129 Chain: "D" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3691 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 476} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.22, per 1000 atoms: 0.62 Number of scatterers: 14820 At special positions: 0 Unit cell: (146.85, 146.85, 112.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2632 8.00 N 2500 7.00 C 9592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 604 " distance=2.07 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 243 " distance=2.02 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 396 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 604 " distance=2.07 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 243 " distance=2.02 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 396 " distance=2.04 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 604 " distance=2.07 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 243 " distance=2.02 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 396 " distance=2.04 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 568 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 604 " distance=2.07 Simple disulfide: pdb=" SG CYS D 219 " - pdb=" SG CYS D 243 " distance=2.02 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 298 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 396 " distance=2.04 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 568 " - pdb=" SG CYS D 577 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 189 " " NAG B 701 " - " ASN B 189 " " NAG C 701 " - " ASN C 189 " " NAG D 701 " - " ASN D 189 " Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.5 seconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 32 sheets defined 20.3% alpha, 46.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.766A pdb=" N ASN A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE A 403 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 404 " --> pdb=" O MET A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER A 437 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE B 403 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 404 " --> pdb=" O MET B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 423 Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER B 437 " --> pdb=" O PRO B 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP C 169 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE C 403 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 404 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 Processing helix chain 'C' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER C 437 " --> pdb=" O PRO C 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN D 83 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP D 169 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE D 403 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 404 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 423 Processing helix chain 'D' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER D 437 " --> pdb=" O PRO D 434 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE A 561 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG A 584 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 563 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 582 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 575 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE A 561 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG A 584 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 563 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 582 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 575 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG A 239 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN A 222 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 237 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 232 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 255 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 234 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A 253 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN A 236 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE A 251 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 238 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG A 257 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 259 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA A 268 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER A 299 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS A 285 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 297 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 287 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP A 295 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN A 364 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 349 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE A 366 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 347 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 368 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG A 466 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 514 through 516 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE B 561 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG B 584 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 563 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 582 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE B 561 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG B 584 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 563 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 582 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR B 220 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG B 239 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN B 222 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU B 237 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR B 232 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU B 255 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE B 234 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 253 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN B 236 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE B 251 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 238 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG B 257 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 259 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA B 268 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER B 299 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS B 285 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 297 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 287 " --> pdb=" O TRP B 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP B 295 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN B 364 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE B 349 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE B 366 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 347 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 368 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AB6, first strand: chain 'B' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG B 466 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 514 through 516 Processing sheet with id=AB8, first strand: chain 'C' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE C 561 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG C 584 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 563 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 582 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 575 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE C 561 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG C 584 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 563 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 582 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 575 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR C 220 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG C 239 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN C 222 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU C 237 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR C 232 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU C 255 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 234 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 253 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C 236 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE C 251 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 238 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG C 257 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 259 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA C 268 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER C 299 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS C 285 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 297 " --> pdb=" O CYS C 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C 287 " --> pdb=" O TRP C 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP C 295 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN C 364 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE C 349 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE C 366 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 347 " --> pdb=" O PHE C 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 368 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AC5, first strand: chain 'C' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG C 466 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 514 through 516 Processing sheet with id=AC7, first strand: chain 'D' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE D 561 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG D 584 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 563 " --> pdb=" O GLU D 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 582 " --> pdb=" O SER D 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE D 561 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG D 584 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 563 " --> pdb=" O GLU D 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 582 " --> pdb=" O SER D 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR D 220 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG D 239 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN D 222 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU D 237 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR D 232 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU D 255 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE D 234 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE D 253 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN D 236 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE D 251 " --> pdb=" O GLN D 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D 238 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG D 257 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL D 259 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA D 268 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER D 299 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS D 285 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU D 297 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D 287 " --> pdb=" O TRP D 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP D 295 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN D 364 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE D 349 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE D 366 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D 347 " --> pdb=" O PHE D 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 368 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 338 through 339 Processing sheet with id=AD4, first strand: chain 'D' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG D 466 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 514 through 516 805 hydrogen bonds defined for protein. 2175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3600 1.33 - 1.46: 3676 1.46 - 1.58: 7732 1.58 - 1.71: 8 1.71 - 1.84: 136 Bond restraints: 15152 Sorted by residual: bond pdb=" CB ILE C 607 " pdb=" CG1 ILE C 607 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CB ILE D 607 " pdb=" CG1 ILE D 607 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CB ILE A 607 " pdb=" CG1 ILE A 607 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CB ILE B 607 " pdb=" CG1 ILE B 607 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CA HIS C 312 " pdb=" C HIS C 312 " ideal model delta sigma weight residual 1.528 1.584 -0.056 1.36e-02 5.41e+03 1.70e+01 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.13: 276 104.13 - 111.66: 6508 111.66 - 119.19: 5584 119.19 - 126.71: 8160 126.71 - 134.24: 116 Bond angle restraints: 20644 Sorted by residual: angle pdb=" N THR D 168 " pdb=" CA THR D 168 " pdb=" C THR D 168 " ideal model delta sigma weight residual 111.71 128.64 -16.93 1.15e+00 7.56e-01 2.17e+02 angle pdb=" N THR B 168 " pdb=" CA THR B 168 " pdb=" C THR B 168 " ideal model delta sigma weight residual 111.71 128.64 -16.93 1.15e+00 7.56e-01 2.17e+02 angle pdb=" N THR C 168 " pdb=" CA THR C 168 " pdb=" C THR C 168 " ideal model delta sigma weight residual 111.71 128.64 -16.93 1.15e+00 7.56e-01 2.17e+02 angle pdb=" N THR A 168 " pdb=" CA THR A 168 " pdb=" C THR A 168 " ideal model delta sigma weight residual 111.71 128.64 -16.93 1.15e+00 7.56e-01 2.17e+02 angle pdb=" N GLU C 407 " pdb=" CA GLU C 407 " pdb=" C GLU C 407 " ideal model delta sigma weight residual 113.15 126.79 -13.64 1.19e+00 7.06e-01 1.31e+02 ... (remaining 20639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8848 18.00 - 36.00: 204 36.00 - 53.99: 52 53.99 - 71.99: 20 71.99 - 89.99: 20 Dihedral angle restraints: 9144 sinusoidal: 3292 harmonic: 5852 Sorted by residual: dihedral pdb=" C THR B 167 " pdb=" N THR B 167 " pdb=" CA THR B 167 " pdb=" CB THR B 167 " ideal model delta harmonic sigma weight residual -122.00 -148.02 26.02 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" C THR C 167 " pdb=" N THR C 167 " pdb=" CA THR C 167 " pdb=" CB THR C 167 " ideal model delta harmonic sigma weight residual -122.00 -148.02 26.02 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" C THR D 167 " pdb=" N THR D 167 " pdb=" CA THR D 167 " pdb=" CB THR D 167 " ideal model delta harmonic sigma weight residual -122.00 -148.02 26.02 0 2.50e+00 1.60e-01 1.08e+02 ... (remaining 9141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 2324 0.200 - 0.400: 40 0.400 - 0.599: 8 0.599 - 0.799: 0 0.799 - 0.999: 4 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA THR B 167 " pdb=" N THR B 167 " pdb=" C THR B 167 " pdb=" CB THR B 167 " both_signs ideal model delta sigma weight residual False 2.53 1.53 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA THR D 167 " pdb=" N THR D 167 " pdb=" C THR D 167 " pdb=" CB THR D 167 " both_signs ideal model delta sigma weight residual False 2.53 1.53 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA THR C 167 " pdb=" N THR C 167 " pdb=" C THR C 167 " pdb=" CB THR C 167 " both_signs ideal model delta sigma weight residual False 2.53 1.53 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 2373 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 398 " -0.290 9.50e-02 1.11e+02 1.30e-01 1.04e+01 pdb=" NE ARG C 398 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 398 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 398 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 398 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 398 " -0.290 9.50e-02 1.11e+02 1.30e-01 1.04e+01 pdb=" NE ARG A 398 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 398 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 398 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 398 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 398 " -0.290 9.50e-02 1.11e+02 1.30e-01 1.04e+01 pdb=" NE ARG B 398 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 398 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 398 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 398 " -0.010 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5007 2.87 - 3.38: 12072 3.38 - 3.88: 23290 3.88 - 4.39: 26759 4.39 - 4.90: 46744 Nonbonded interactions: 113872 Sorted by model distance: nonbonded pdb=" N MET C 313 " pdb=" O MET C 313 " model vdw 2.359 2.496 nonbonded pdb=" N MET B 313 " pdb=" O MET B 313 " model vdw 2.359 2.496 nonbonded pdb=" N MET A 313 " pdb=" O MET A 313 " model vdw 2.359 2.496 nonbonded pdb=" N MET D 313 " pdb=" O MET D 313 " model vdw 2.359 2.496 nonbonded pdb=" N SER A 459 " pdb=" N SER A 460 " model vdw 2.566 2.560 ... (remaining 113867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 42.820 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.088 15152 Z= 0.822 Angle : 1.504 16.930 20644 Z= 1.054 Chirality : 0.094 0.999 2376 Planarity : 0.007 0.130 2636 Dihedral : 10.394 89.988 5308 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.23 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 1976 helix: 1.52 (0.28), residues: 292 sheet: 0.88 (0.19), residues: 724 loop : 0.02 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP D 318 HIS 0.004 0.001 HIS C 596 PHE 0.019 0.004 PHE A 523 TYR 0.035 0.005 TYR D 414 ARG 0.003 0.001 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.749 Fit side-chains REVERT: A 513 ASP cc_start: 0.8638 (p0) cc_final: 0.8352 (p0) REVERT: B 513 ASP cc_start: 0.8643 (p0) cc_final: 0.8353 (p0) REVERT: C 513 ASP cc_start: 0.8646 (p0) cc_final: 0.8345 (p0) REVERT: D 513 ASP cc_start: 0.8638 (p0) cc_final: 0.8344 (p0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3018 time to fit residues: 103.0630 Evaluate side-chains 152 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 123 GLN C 123 GLN D 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15152 Z= 0.241 Angle : 0.598 7.147 20644 Z= 0.332 Chirality : 0.046 0.141 2376 Planarity : 0.004 0.030 2636 Dihedral : 4.831 21.977 2240 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.72 % Allowed : 4.01 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 1976 helix: 2.85 (0.29), residues: 296 sheet: 0.78 (0.18), residues: 756 loop : -0.33 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.002 0.001 HIS D 596 PHE 0.021 0.002 PHE B 523 TYR 0.015 0.002 TYR A 414 ARG 0.002 0.001 ARG D 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.772 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 164 average time/residue: 0.3024 time to fit residues: 71.8960 Evaluate side-chains 136 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 196 optimal weight: 0.3980 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15152 Z= 0.287 Angle : 0.573 5.776 20644 Z= 0.312 Chirality : 0.047 0.146 2376 Planarity : 0.004 0.036 2636 Dihedral : 4.576 20.274 2240 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.79 % Allowed : 4.51 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 1976 helix: 3.20 (0.28), residues: 296 sheet: 0.60 (0.18), residues: 764 loop : -0.74 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 318 HIS 0.004 0.002 HIS C 194 PHE 0.017 0.002 PHE B 523 TYR 0.018 0.002 TYR D 414 ARG 0.002 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.721 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 172 average time/residue: 0.2825 time to fit residues: 70.9248 Evaluate side-chains 145 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 ASN B 589 ASN C 589 ASN D 589 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15152 Z= 0.340 Angle : 0.585 6.089 20644 Z= 0.315 Chirality : 0.048 0.151 2376 Planarity : 0.004 0.043 2636 Dihedral : 4.576 19.096 2240 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.87 % Allowed : 4.87 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1976 helix: 3.15 (0.28), residues: 296 sheet: 0.38 (0.18), residues: 760 loop : -1.00 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.004 0.002 HIS B 194 PHE 0.018 0.002 PHE C 523 TYR 0.016 0.002 TYR A 414 ARG 0.002 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.723 Fit side-chains outliers start: 40 outliers final: 24 residues processed: 148 average time/residue: 0.2627 time to fit residues: 58.6795 Evaluate side-chains 148 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15152 Z= 0.217 Angle : 0.518 5.092 20644 Z= 0.278 Chirality : 0.046 0.143 2376 Planarity : 0.004 0.044 2636 Dihedral : 4.356 16.608 2240 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.72 % Allowed : 6.30 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1976 helix: 3.35 (0.29), residues: 296 sheet: 0.47 (0.18), residues: 768 loop : -0.97 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.002 0.001 HIS B 596 PHE 0.014 0.002 PHE A 523 TYR 0.012 0.002 TYR D 571 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.796 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 147 average time/residue: 0.2638 time to fit residues: 59.4283 Evaluate side-chains 136 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 520 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15152 Z= 0.200 Angle : 0.501 4.861 20644 Z= 0.270 Chirality : 0.046 0.141 2376 Planarity : 0.004 0.042 2636 Dihedral : 4.212 15.301 2240 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.22 % Allowed : 6.59 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1976 helix: 3.46 (0.28), residues: 292 sheet: 0.47 (0.18), residues: 764 loop : -1.04 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.002 0.001 HIS C 194 PHE 0.014 0.002 PHE D 523 TYR 0.013 0.001 TYR B 464 ARG 0.001 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.675 Fit side-chains outliers start: 31 outliers final: 23 residues processed: 157 average time/residue: 0.2603 time to fit residues: 62.5719 Evaluate side-chains 167 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15152 Z= 0.180 Angle : 0.484 4.854 20644 Z= 0.260 Chirality : 0.045 0.139 2376 Planarity : 0.004 0.044 2636 Dihedral : 4.103 15.071 2240 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.72 % Allowed : 7.45 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1976 helix: 3.48 (0.28), residues: 292 sheet: 0.47 (0.18), residues: 772 loop : -1.04 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 274 HIS 0.002 0.001 HIS D 194 PHE 0.013 0.002 PHE D 523 TYR 0.012 0.001 TYR C 464 ARG 0.001 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.742 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 156 average time/residue: 0.2592 time to fit residues: 61.4986 Evaluate side-chains 168 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 520 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15152 Z= 0.270 Angle : 0.525 4.870 20644 Z= 0.283 Chirality : 0.046 0.140 2376 Planarity : 0.004 0.043 2636 Dihedral : 4.240 15.836 2240 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.29 % Allowed : 7.74 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1976 helix: 3.34 (0.28), residues: 292 sheet: 0.43 (0.19), residues: 756 loop : -1.14 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.003 0.001 HIS D 194 PHE 0.014 0.002 PHE B 523 TYR 0.022 0.002 TYR D 464 ARG 0.002 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.904 Fit side-chains outliers start: 32 outliers final: 24 residues processed: 156 average time/residue: 0.2570 time to fit residues: 61.3557 Evaluate side-chains 164 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15152 Z= 0.240 Angle : 0.512 4.846 20644 Z= 0.276 Chirality : 0.046 0.138 2376 Planarity : 0.004 0.043 2636 Dihedral : 4.229 15.958 2240 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.01 % Allowed : 7.74 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1976 helix: 3.32 (0.28), residues: 292 sheet: 0.45 (0.19), residues: 756 loop : -1.13 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.003 0.001 HIS D 194 PHE 0.013 0.002 PHE D 523 TYR 0.022 0.002 TYR D 464 ARG 0.001 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.781 Fit side-chains outliers start: 28 outliers final: 24 residues processed: 156 average time/residue: 0.2594 time to fit residues: 62.0791 Evaluate side-chains 164 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 561 ILE Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 158 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15152 Z= 0.219 Angle : 0.504 4.855 20644 Z= 0.273 Chirality : 0.046 0.135 2376 Planarity : 0.004 0.042 2636 Dihedral : 4.183 15.799 2240 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.72 % Allowed : 8.02 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1976 helix: 3.25 (0.28), residues: 292 sheet: 0.50 (0.18), residues: 764 loop : -1.19 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 274 HIS 0.002 0.001 HIS A 194 PHE 0.013 0.002 PHE D 523 TYR 0.024 0.002 TYR B 464 ARG 0.001 0.000 ARG D 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.618 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 156 average time/residue: 0.2648 time to fit residues: 62.6122 Evaluate side-chains 168 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 561 ILE Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120832 restraints weight = 17404.221| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.04 r_work: 0.3261 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15152 Z= 0.172 Angle : 0.493 6.357 20644 Z= 0.263 Chirality : 0.045 0.133 2376 Planarity : 0.004 0.042 2636 Dihedral : 4.095 15.377 2240 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.72 % Allowed : 8.60 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 1976 helix: 3.39 (0.28), residues: 292 sheet: 0.54 (0.18), residues: 772 loop : -1.18 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 274 HIS 0.004 0.001 HIS C 312 PHE 0.013 0.002 PHE A 523 TYR 0.021 0.001 TYR D 464 ARG 0.001 0.000 ARG B 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.87 seconds wall clock time: 60 minutes 6.29 seconds (3606.29 seconds total)